04 September 2012

The Molecular Ecologist: Isolating isolation by distance

And now I present my first "real" post as a contributor at the Molecular Ecologist, a discussion of a new review article pointing out that population geneticists aren't doing a great job dealing with one of the best-known patterns in population genetics, isolation by distance, or IBD. You may recall that I discussed IBD in a more historical context way back in the day on this very website. It's simply a pattern in which populations located close to each other are more genetically similar than populations farther away from each other, which arises because most critters (or their seeds, or larvae, or pollen) are less likely to move longer distances. But IBD can be conflated with a number of other patterns population geneticists often try to detect:

So let’s say you’ve collected genetic data from sites on either side of a line you think might be biologically significant—a pretty standard-issue population genetics study. You run your data through Structure, and find two clusters of collection sites that line up pretty well with that Line of Hypothesized Biological Significance. As a followup, you conduct an AMOVA with the collection sites grouped according to their placement by Structure, and you find that the clusters explain a significant fraction of the total genetic variation in your data set. Therefore, you conclude that the LHBS is, in fact, a significant barrier to dispersal.

Except that as we’ve just discussed, everything you’ve just found could be a consequence of simple IBD plus the fact that you’ve structured your sampling so that your LHBS happens to bisect the landscape you’re studying. And just to add to the frustration, even if you’d started out by testing for IBD before you started with all of the tests for population structure, a significant result in a Mantel test for IBD wouldn’t necessarily mean that population structure wasn’t there.

To find out how the author of the new review article suggests we deal with the complications outlined above, go read the whole thing.◼

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